tbuckley/cabot-search huggingface dataset:
MODL-40. CLONAL ARCHITECTURE, TRANSCRIPTIONAL CELLULAR STATES AND IN-VITRO DRUG RESPONSE IN GLIOBLASTOMA
Authors: Youjin Song, Yelyzaveta Miller-Michlits, Lisa Greutter, Barbara Kiesel, Daniela Loetsch-Gojo, Vivian Redl, Johanna Gesperger, Jana Breu, Do-Hyun Nam, Georg Widhalm, Jason K Sa, Adelheid Woehrer
Journal: Neuro-Oncology (2023)

Abstract Seventy-five multiregional tumors from 20 representative GBM patients (female/male ratio = 0.75, median age= 63 ys) were profiled using deep whole-exome sequencing with a nominal coverage of &amp;gt; 300x. The clonal complexity of each individual tumor was measured by calculating the molecular distance using the Euclidean distance of all possible paired regions based on somatic mutational profiles. Among them, fresh tumor slices of 4 patients were cultured in minimal essential media and treated with 4.2 Gy plus 200 µM temozolomide for 48 hours. Spatial Transcriptomics was performed on matched tumor slices with and without treatment. Molecular characterization of multiregional tumors revealed two patterns of evolutionary trajectory, linear and branched (linear: 8 cases, branched: 8 cases) among 16 patients. Tumors with branched evolution demonstrated considerable levels of molecular divergence, determined by high molecular distance and a low number of mutations that were shared among all regions. In-vitro drug response varied considerably between patients based on cell proliferation (minus 0.5 to 13.8 %), apoptotic rates (30.1 to 44.4 %), and cell viability (minus 7.8 to 34.1 %). Under treatment pressure an increase of mesenchymal cellular states with peculiar redistribution of transcriptional patterns and increased clonal complexity was observed. In sum, we report on an ongoing study in glioblastoma that seeks to link the clonal architecture with spatially-resolved transcriptional patterns and in-vitro drug response. Our study will provide new insights into the clinical relevance of the clonal composition of this deadly cancer.
CNSC-23. ROLE OF GLIAL PH-DEPENDENT METABOLIC REGULATION IN GLIOMA PROGRESSION
Authors: Qi Ye, Heavin Oh, Tiffany Choy, Christine Madamba, Akdes Serin-Harmanci, Ganesh Rao, Hyun Kyoung Lee
Journal: Neuro-Oncology (2023)

Abstract Malignant glioma is a devastating brain cancer with barely any improvement in prognosis over decades. One key mechanism for glioma invasiveness is the dynamic metabolic communication between glioma and surrounding cells shaping the tumor microenvironment. While extracellular acidosis is a pathological hallmark of glioma, pH-dependent mechanisms underlying tumor metabolic reprogramming remain poorly defined. Our study focuses on a glial-enriched sodium-bicarbonate cotransporter, Slc4a4, which was previously identified as intracellular and extracellular pH regulator. While Slc4a4-mediated pH regulation is important for physiological brain function and responses after injury, its role in glioma progression is largely undefined. To begin addressing this question, we analyzed The Cancer Genome Atlas (TCGA) database, finding high Slc4a4 expression correlates with prolonged survival in glioma patients. Corroboratively, Slc4a4 gain-of-function (GOF) drastically decreases tumorigenesis and angiogenesis in patient-derived-xenograft and CRISPR-mediated de novo mouse glioma models. These results are further complemented by loss-of-function (LOF) studies using glial-specific Slc4a4 knockout mice, suggesting an inhibitory role of Slc4a4 in glioma growth and associated angiogenesis. A combination of unbiased metabolomic and cancer-targeted proteomic profiling of Slc4a4 GOF/LOF mouse glioma reveals an inverse correlation between Slc4a4 and a key lipid metabolism protein, FABP5 (Fatty Acid Binding Protein 5), which is coupled with dysregulated lipid metabolism. Moreover, analysis of TCGA database shows inverse expression and survival correlation of Slc4a4 and FABP5 in glioma patients. Further functional study shows that overexpression of FABP5 reverses Slc4a4’s inhibitory effects on glioma growth in immunocompetent mouse glioma model, supporting a functional antagonism between Slc4a4 and FABP5. Together, our study indicates that Slc4a4 plays a protective role in glioma progression by regulating metabolic activities, providing critical insights into pH-dependent metabolic reprogramming in glioma.
CSIG-25. OVERCOMING RESISTANCE TO THERAPIES TARGETING THE MAPK PATHWAY IN GLIOBLASTOMA
Authors: Severa Bunda, Kenneth Aldape, Gelareh Zadeh
Journal: Neuro-Oncology (2023)

Abstract Capicua (CIC) is a transcriptional repressor that inhibits expression of genes induced by receptor tyrosine kinase (RTK) activation. RTK/Ras/ERK signaling is one of the most tumorigenic pathways in cancer. In fact, the aggressive nature of the most common and lethal brain tumor, glioblastoma (GBM), has been attributed to hyperactivation of RTK. While CIC is mutated in other tumor types, we found that CIC has a tumor-suppressive function in GBM through an alternative mechanism. We show that Ras/ERK promotes degradation of CIC, resulting in de-repression of CIC targets and amplification of the tumorigenic Ras/ERK signal. Importantly, we show that sustained MEK/ERK inhibition fails to restore CIC protein levels desensitizing from upstream RTK/MEK/ERK inhibition. Our findings suggest the lack of efficacy of MEK/ERK inhibitors in GBM in the clinical context is due to the loss of CIC-mediated repression, hence exposing CIC as a potential therapeutic target in combination with MEK/ERK inhibitors. To uncover targetable pathways that stabilize CIC and sensitize towards MEK/ERK inhibitors in GBM we need to understand how CIC works and causes gene repression. We identified a novel CIC binding partner, Yin Yang 1 (YY1), a context dependent transcription factor important in GBM. We found that YY1/CIC binding co-regulates repression of genes downstream of RTK/Ras/ERK activation important in tumorigenesis. Importantly we uncovered a targetable pathway that leads to stabilization of CIC/YY1 on its target DNA which sensitizes towards MEK/ERK inhibition. These data provide insight into more effective therapeutic avenues to stabilize the CIC/YY1 co-repressor complex and re-sensitize towards RTK/Ras/MEK/ERK inhibition in GBM and likely in other tumors characterized with hyperactive Ras/ERK signaling and CIC loss.
TMET-10. INVESTIGATING HOW GLIOBLASTOMA TUMOUR CELLS EXPLOIT THEIR METABOLIC MICROENVIRONMENT
Authors: Chloe Shard, Rebecca Ormsby, Santosh Poonnoose, John Toubia, Paul Trim, Lisa Ebert, Ashwini Patil, Guillermo Gomez
Journal: Neuro-Oncology (2023)

Abstract A significant challenge in neuro-oncology is identifying the metabolic fuel sources that underpin glioblastoma malignancy. Metabolic reprogramming is a hallmark of tumorigenesis, providing malignant cells with an adaptation advantage to survive and grow under environmental stresses, including anti-cancer therapies. Incorporating single-cell RNA sequencing data from 56 glioblastoma patient biopsies, we have identified distinct subpopulations of malignant cells which diverge in their metabolic activities. These metabolic subpopulations are conserved across patient datasets but vary in abundance from patient to patient, contributing to glioblastoma heterogeneity. We are also employing spatial transcriptomics to build a map of the metabolic tumour landscape. This analysis showed that these malignant sub-populations occupy distinct spatial regions in the tumour landscape. Environmental influences like distance to blood vessels, which impact oxygen and nutrient supply, can vary significantly between regions. This suggests that as malignant cells colonise different regions of the tumour, they modify their metabolism as an adaption response. Importantly these niches vary in their compositions of native brain and immune cells, contributing to the diverse ecosystems inhabited by these malignant subpopulations. The next steps are to explore the specific metabolite dependencies of these tumour cells by mass spectrometry imaging and identify metabolite fluxes within the microenvironment that we can target therapeutically.
NCMP-10. DEXAMETHASONE: A TOOL AND A PROBLEM IN GLIOBLASTOMA MANAGEMENT
Authors: Amro Mohammad, Sukhdeep Jatana, Rawan Sakalla, William Davalan, Roy Khalaf, Hongda Li, Rebecca Aberra, Mathew Carias, Tariq Al-saadi, Natalia Guevara-Moriones, Miguel Angel Ruiz-Barrera, Chritina Mindru, Roberto Diaz
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) patient morbidity and overall survival (OS) are associated with dexamethasone use. We studied dexamethasone-associated hyper-glycemia, leukocytosis, and accompanying complications in the peri-operative period. We also examined the effect of metformin treatment on GBM patient OS. We retrospectively studied 243 GBM patients admitted between 2014-2018. Patients with peri-operative glucose measurements and adequate follow-up to assess for complications were included. Metformin was used for treatment of diabetes or in the management of glucocorticoid-induced hyper-glycemia. Kaplan-Meier curves and log-rank p test were used for univariate analysis. Cox-proportional hazards model was used to generate adjusted hazard ratios for multivariate analysis. Dexamethasone dose was associated with hyper-glycemia and leukocytosis post-operatively. Poor glycemic control was associated with increased odds of 30-day any complication on univariate analysis and 30-day any complication and increased length of stay on multivariate analysis. We then demonstrated that metformin improved OS in methylated O6-methylguanine DNA methyltransferase gene (MGMT) promoter tumor patients (652 days, 95% CI 327 – 897, n = 25 vs 394 days, 95% CI 210 – 513, n = 63; P = .049). Non-diabetic MGMT-methylated tumor patients treated with metformin also had an improved median OS of 736 days, 95% CI 365 – 1036, n = 11 vs 395 days, 95% CI 210 – 513, n = 66; P = .01). Overall, peri-operative hyper-glycemia and higher average dexamethasone use are associated with poor glycemic control and leukocytosis. As a result, dexamethasone can increase the risk of peri-operative complications in GBM patients. Avoiding hyper-glycemia by limiting dexamethasone use or using Metformin may decrease the risk of complications and improve OS.
TMIC-24. FERROPTOSIS INDUCES IMMUNOGENIC CELL DEATH AND SYNERGIZES WITH CD47 BLOCKADE TO REPROGRAM THE GLIOMA MICROENVIRONMENT
Authors: Colin Sperring, Michael Argenziano, Matei Banu, Athanassios Dovas, Angeliki Mela, Wenting Zhao, Julia Furnari, Brianna Pereira, Casey Ager, Mitchell Yeary, Ben Shapiro, Corina Kotidis, Oluwaseyi Adeyuan, Dominique Higgins, Pavan Upadhyayula, Aayushi Mahajan, Nelson Humala, Benjamin Izar, Peter Sims, Jeffrey Bruce, Peter Canoll
Journal: Neuro-Oncology (2023)

Abstract Immunotherapy has thus far proven ineffective in glioblastoma, in part due to the immune cold tumor microenvironment. Here we demonstrate that ferroptosis specifically targets a quiescent, immunosuppressive astrocyte-like glioma population and can therefore be used as a novel inducer of immunogenic cell death to repolarize the immune microenvironment by promoting tumor cell phagocytosis and antigen presentation. First, we characterized the immunogenic effects of ferroptosis by using a glioma cell-myeloid cell co-culture system and patient-derived organotypic slice cultures and performed phagocytosis assays, flow-cytometry, immunohistochemistry, cytokine arrays and single cell RNAseq. GPX4-dependent ferroptosis induced translocation of the pro-phagocytic eat-me signal calreticulin in both murine glioma cells and human tissue samples. Ferroptotic-driven tumor cell death reprogramed local myeloid populations to promote glioma phagocytosis, MHCII-driven antigen presentation, and paracrine cytokine signaling involved in T-cell recruitment. Local delivery of RSL3, a GPX4 inhibitor, in a murine glioma model polarized myeloid cells to a pro-phagocytic phenotype and significantly increased intra-tumoral levels of CD4+ and CD8+ T-cells. Astrocytic-like tumor cells upregulate CD47 as a mechanism to evade phagocytosis. Therefore, we combined ferroptosis with an anti-CD47 monoclonal antibody (aCD47) to enhance reprogramming of the immune cold microenvironment. In an orthotopic murine glioma model, adding aCD47 to RSL3 led to significantly increased tumor phagocytosis, antigen presentation and prolonged survival. Thus, we demonstrate that local delivery of ferroptosis-inducing agents in conjunction with CD47 blockade is an effective multi-modality therapeutic regimen capable of reversing the immunosuppressive glioma microenvironment.
RADT-31. OPTIMAL TIMING OF CHEMORADIATION AFTER RESECTION OR BIOPSY OF GLIOBLASTOMAS: A NATIONWIDE POPULATION-BASED STUDY
Authors: Tae Hoon Roh, Yeonhu Lee, Se-Hyuk Kim
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND The optimal time interval of concomitant chemoradiotherapy (CCRT) after surgery for newly diagnosed glioblastoma (GBM) patients remains controversial. This study was aimed to assess whether the interval between surgery and CCRT leads to a survival difference. METHODS Using the Korean National Health Insurance Research Database, 3,586 patients diagnosed with GBM in South Korea from 2008 to 2021 were retrospectively reviewed. The eligibility criteria were GBM-diagnosed patients who underwent surgical resection or biopsy and received CCRT (with temozolomide (TMZ)) within 6 weeks thereafter. Patients were divided into two groups based on interval between surgery and CCRT initiation: early radiotherapy (RT) within 21 days and late RT &amp;gt; 21 days. Patients were separately examined by the type of surgery – biopsy alone or resective surgery. Overall survival (OS) was estimated using the Kaplan-Meier method and log-rank tests. Univariable and Multivariable Cox regression analyses were performed to assess the impact of the covariables on OS. RESULTS The median OS for early RT group was 20.47 months compared to 17.94 months of late RT group (Log rank P value of 0.0002). Early RT was associated with prolonged OS in multivariable analysis adjusting age, sex, length of stay in hospital after surgery, and the procedure type of biopsy or tumor resection. On the contrary, subgroup analysis showed that patients who received early RT after biopsy showed higher OS than the patients who received late RT (15.93 months vs. 11.83 months). CONCLUSION Patients who received CCRT after 21 days of operation showed better OS than those with earlier CCRT initiation. In contrast, in the group patients who received biopsy alone showed better outcomes when started RT within 21 days. This result suggests that optimal timing of initiation of CCRT after surgery for glioblastoma may be different according to the remnant tumors.
TMIC-85. TGFB2 AND IFNGR2 MRNA EXPRESSION LEVELS IN THE TUMOR MICROENVIRONMENT (TME) PROGNOSITICALLY IMPACT OS IN PEDIATRIC DIPG PATIENTS
Authors: SanJive Qazi, Vuong Trieu
Journal: Neuro-Oncology (2023)

Abstract DIPG patients expressed significantly higher levels of TGFB2 and IFNGR2 than control pons samples and the expression profile indicated higher levels of TGFB2 than TGFB1 and TGFB3 in DIPG patients suggesting TGFB2 mRNA level is preferentially increased in DIPG patients. TGFB2 is a prognostic indicator (HR for patients in the TGFB2high group of DIPG patients = 2.88 (1.12-7.39); P = 0.028) for poor overall survival (OS) independent of IFNGR2 levels, the age of the patient, and the significant interaction effect observed between IFNGR2 and TGFB2. Predictive modeling using the Cox regression parameters showed that the context of low expression of IFNGR2, TGFB2low resulted in more favorable OS times compared to TGFB2high whereby the median OS time of 11 months for the TGFB2low group of patients was greater than the upper 95% confidence limit for the TGFB2high group of patients (Median = 7 months; Upper 95% Confidence interval = 10 months). At higher levels of IFNGR2 expression, the TGFB2high group of patients exhibited a median OS time of 15 months that was within the (95% confidence interval for the TGFB2low group of patients (Median = 13 months; 95% CI = 10-17 months). Worse survival outcomes comparing DIPG patients with high versus low TGFB2 levels in the context of low levels of IFNGR2 levels suggest that abrogating the TGFB2 mRNA expression in the immunologically cold tumor microenvironment indicated by low levels of IFNGR2 expression can potentially treat pediatric DIPG patients. Furthermore, DIPG patients with low levels of JAK1 or STAT1 mRNA expression in combination with TGFB2high also exhibited poor OS outcomes suggesting that the inclusion of (Interferon-gamma) IFNγ to stimulate and activate JAK1 and STAT1 in anti-tumor immune cells present the brainstem tumor microenvironment can enhance the effect of TGFB2 blockade.
NIMG-79. DIFFERENTIATION OF SUBTYPES IN AFULLY AUTOMATED DEEP LEARN TUMORS USING PREOPERATIVEM RIMAGES ING APPROACH FOR ACCURATE PRIMARY INTRACRANIAL
Authors: Yanong Li
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Intracranial germ cell tumors (iGCTs) are divided into germinomas (GEs) and nongerminomatous germ cell tumors (NGGCTs), each having distinct treatments and prognoses. However, predictive biomarkers for differentiation are limited. Here, we aim to develop a deep learning (DL) model that can automatically differentiate GEs from NGGCTs using preoperative magnetic resonance (MR) images and analyzing how our model improved clinical decision making among five physicians. METHODS: This multicenter study included patients with pathology-confirmed iGCTs for the developed set (total n = 280), which was split into training (n = 200) and testing datasets (n= 80), and three independent validation datasets (n = 64), respectively. We developed a DL model based on 3D nnU-Net and preoperative MR images to differentiate GEs from NGGCTs. To evaluate the clinical value of the DL model, five physicians' accuracy and level of consistency in identifying tumor types were compared in the testing and three validation datasets, with and without referring to the DL model’s output. RESULTS The DL model achieved AUCs of 0.950, 0.921, 0.869, and 0.905 in the testing and three validation datasets, respectively, which is superior to using conventional information including MR features and clinical information (AUC=0.768, P=0.009). The physicians’ diagnostic performance improved from an average AUC of 0.695 without reference to the DL output to 0.842 using the DL output in the testing and independent validation datasets (21.2% improvement, P=0.014). CONCLUSIONS We developed and validated a DL model using a large dataset to accurately differentiate GEs from NGGCTs using preoperative MR images.
NIMG-48. ASSOCIATIONS BETWEEN HETEROGENEITY OBSERVED IN O-6-METHYLGUANINE-DNA METHYLTRANSFERASE (MGMT) ASSAY MEASUREMENTS AND MGMT-BASED IMAGING SIGNATURE BASED ON MRI AND DEEP LEARNING
Authors: Sanjay Saxena, Anahita Fathi Kazerooni, Erik Toorens, Spyridon Bakas, Hamed Akbari, Elizabeth Mamourian, Tapan Ganguly, MacLean P Nasrallah, Christos Davatzikos
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND O-6-methylguanine-DNA methyltransferase(MGMT), a gene promoter, corresponds with the efficacy of standard therapy for Glioblastoma (GBM) patients. If a single sample is sequenced, an appropriate diagnosis of MGMT methylation may be hampered by intratumoral heterogeneity. This work proposes a non-invasive in-vivo estimation of MGMT methylation using deep learning and multi-parametric MRI (mpMRI). Further, it quantifies spatial heterogeneity and establishes the associations between MGMT assay measurement and MGMT imaging signature heterogeneity. METHODS For this study, mpMRI structural scans (T1, T2, FLAIR and T1-Gd) of 498 newly diagnosed GBM patients were considered. These patients underwent surgical tumor resection, and MGMT methylation testing was retrospectively collected. By overlaying local and regional 2D patches of size 32 X 32 over the whole tumor on mpMRI scans, a 10-fold cross-validated deep convolutional neural network model was trained considering five layers on the discovery cohort (n=458). The trained model was applied to an independent multi-sample cohort (n=40) to compute the MGMT methylation at the pixel level for imaging-derived maps generation and heterogeneity quantification. The independent cohort included the patients for whom multiple tissue specimens were sequenced for MGMT methylation. RESULTS The patch-based deep model produced an area under the ROC curve of 0.76 (95% CI: 0.71–0.82) for MGMT status prediction. This model showed a strong association between homogeneously MGMT methylated and heterogeneous cases with MGMT Assay measurement of multiple samples with Pearson’s correlation coefficients of 0.64 (p &amp;lt; 0.05) and 0.78 (p &amp;lt; 0.01), respectively. Further, heterogeneity with a significantly higher variance was also observed in heterogeneous cases in developed MGMT imaging signature. CONCLUSION The proposed model efficiently determines MGMT promoter methylation and quantifies GBM spatial heterogeneity non-invasively. Also, it showed a significant association between the heterogeneity observed in MGMT-based imaging signature and MGMT assay measurements.
NCOG-23. ASSESSMENT OF NON-MEASURABLE DISEASE IN HIGH-GRADE GLIOMA: RANO-BASED 2D VS. 3D VOLUMETRICS
Authors: Maguy Farhat, Melissa Chen, Maria Gule, Wasif Talpur, Holly Langshaw, Victoria White, Caroline Chung
Journal: Neuro-Oncology (2023)

Abstract Non-measurable disease (NMD) in High grade glioma (HGG), defined as "longest perpendicular dimension of less than 10 mm”, is a limitation of RANO criteria that limits trial enrollment and biases trial populations to exclude patients with smaller tumors that eventually become measurable. Volumetric (3D) measurements may improve sensitivity and precision for measuring HGG of all sizes, however there is limited data comparing volumetric to 2D RANO measurements. AIMS: To investigate the correlation between RANO-based bidimensional 2D and 3D volumetric measurements in the postoperative setting of patients with HGG, including patients with NMD. METHODS: Contrast-enhanced (CE) postoperative and radiotherapy planning MRIs were utilized for 2D RANO measurements by neuroradiologists and volumetric (3D) measurements extracted from segmentations of CE disease. Pearson’s correlation between the 2D and 3D measurements were evaluated at each time point. The percentage of NMD based on RANO criteria and the range of tumor volumes for the NMD cases were reported. RESULTS: For 59 patients, there was lower concordance in the 2D and 3D measures at the postoperative MRI time point (Pearson =0.46) compared to the treatment planning MRI time point (Pearson=0.81). Interestingly, the postoperative time point had a higher percentage of NMD of 38% with the mean tumor volume of 13 cm3 (range: 0-21 cm3) compared to the treatment planning MRI with percentage NMD of 8% and mean tumor volume of 9 cm3 (range: 6-13cm3). CONCLUSION: In this study, higher rate of agreement was observed between RANO-based 2D and 3D volumetric tumor measurements at the time point of MR simulation when there was lower rate of NMD, suggesting NMD may contribute to the discrepancy between 2D and 3D measurements. Volumetric measurement tools may be a superior approach to improve the assessment especially of NMD in the postoperative period, improving trial enrollment for these patients.